preparation of non-10x reference data and isoform-level quantitation

[bumproo]

Hi,

I'm trying to process some crab-eating macaque data using that genome and the corresponding ensembl annotation. I see in your documentation that 10x reference is necessary for sockeye but I don't believe one of those is available for my species. I have been able to get my data to run through the pipeline by making some adjustments to the ensembl target. For example, I had to change chromosome names from "1" to "chr1" in both fasta and gtf. That said, my output/sample/matrix/ processed and counts files are incorrect. Each has only 14 rows that are derived from gene type rather than gene symbol. I was wondering if you have any suggestions for preparing the gtf file so that it works with sockeye?

In addition, I'm also wondering about isoform-level quantitation rather than gene-level. Is this possible?

thanks Charlie